Mercurial > hg > orthanc-book
changeset 363:9c28eeab2db6
removed sudo from docker
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 31 Mar 2020 17:27:55 +0200 |
| parents | 022d59428ea3 |
| children | 234de55ed125 |
| files | Sphinx/source/users/advanced-rest.rst Sphinx/source/users/docker.rst |
| diffstat | 2 files changed, 21 insertions(+), 21 deletions(-) [+] |
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--- a/Sphinx/source/users/advanced-rest.rst Tue Mar 31 15:13:35 2020 +0200 +++ b/Sphinx/source/users/advanced-rest.rst Tue Mar 31 17:27:55 2020 +0200 @@ -272,4 +272,4 @@ writing this configuration to, say, ``/tmp/prometheus.yml``, then type:: - $ sudo docker run -p 9090:9090 -v /tmp/prometheus.yml:/etc/prometheus/prometheus.yml --rm prom/prometheus:v2.7.0 + $ sudo run -p 9090:9090 -v /tmp/prometheus.yml:/etc/prometheus/prometheus.yml --rm prom/prometheus:v2.7.0
--- a/Sphinx/source/users/docker.rst Tue Mar 31 15:13:35 2020 +0200 +++ b/Sphinx/source/users/docker.rst Tue Mar 31 17:27:55 2020 +0200 @@ -51,7 +51,7 @@ The following command will start the core of Orthanc, with all the plugins disabled:: - $ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc + $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc Once Orthanc is running, use Mozilla Firefox at URL http://localhost:8042/ to interact with Orthanc. The default username @@ -61,18 +61,18 @@ development is in continuous progress. Do not forget to regularly update the Docker image to benefit from the latest features:: - $ sudo docker pull jodogne/orthanc + $ docker pull jodogne/orthanc If more stability is required, you can select the official release of Orthanc to be run:: - $ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.6.0 + $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.6.0 Passing additional command-line options (e.g. to make Orthanc verbose) can be done as follows (note the ``/etc/orthanc`` option that is required for Orthanc to find its configuration files):: - $ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc /etc/orthanc --verbose + $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc /etc/orthanc --verbose Usage, with plugins enabled @@ -84,7 +84,7 @@ implementation <dicomweb>`, and its :ref:`whole-slide imaging viewer <wsi>`:: - $ sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins + $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins Fine-tuning the configuration @@ -98,12 +98,12 @@ You can generate a custom configuration file for Orthanc as follows:: - $ sudo docker run --rm --entrypoint=cat jodogne/orthanc /etc/orthanc/orthanc.json > /tmp/orthanc.json + $ docker run --rm --entrypoint=cat jodogne/orthanc /etc/orthanc/orthanc.json > /tmp/orthanc.json Then, edit the just-generated file ``/tmp/orthanc.json`` and restart Orthanc with your updated configuration:: - $ sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc + $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc Making the Orthanc database persistent @@ -115,7 +115,7 @@ container to some path in the filesystem of your Linux host, e.g.:: $ mkdir /tmp/orthanc-db - $ sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.6.0 + $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.6.0 Whole-slide imaging support @@ -125,13 +125,13 @@ whole-slide imaging (WSI) <wsi>`. For instance, the following command will start the WSI viewer plugin transparently together with Orthanc:: - $ sudo docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins + $ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins Note that we gave the name ``orthanc-wsi`` to this new Docker container. Then, the Dicomizer command-line tool can be invoked as follows:: - $ sudo docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.tif:/tmp/Source.tif:ro jodogne/orthanc-plugins --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ /tmp/Source.tif + $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.tif:/tmp/Source.tif:ro jodogne/orthanc-plugins --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ /tmp/Source.tif This command needs a few explanations: @@ -159,7 +159,7 @@ instruct the Dicomizer to use `OpenSlide <https://openslide.org/>`__ to decode it by adding the ``--openslide`` option:: - $ sudo docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.svs:/tmp/Source.svs:ro jodogne/orthanc-plugins --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ --openslide=libopenslide.so /tmp/Source.svs + $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.svs:/tmp/Source.svs:ro jodogne/orthanc-plugins --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ --openslide=libopenslide.so /tmp/Source.svs PostgreSQL and Orthanc inside Docker @@ -167,20 +167,20 @@ It is possible to run both Orthanc and PostgreSQL inside Docker. First, start the official PostgreSQL container:: - $ sudo docker run --name some-postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pgpassword --rm postgres + $ docker run --name some-postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pgpassword --rm postgres Open another shell, and create a database to host the Orthanc database:: - $ sudo docker run -it --link some-postgres:postgres --rm postgres sh -c 'echo "CREATE DATABASE orthanc;" | exec psql -h "$POSTGRES_PORT_5432_TCP_ADDR" -p "$POSTGRES_PORT_5432_TCP_PORT" -U postgres' + $ docker run -it --link some-postgres:postgres --rm postgres sh -c 'echo "CREATE DATABASE orthanc;" | exec psql -h "$POSTGRES_PORT_5432_TCP_ADDR" -p "$POSTGRES_PORT_5432_TCP_PORT" -U postgres' You will have to type the password (cf. the environment variable ``POSTGRES_PASSWORD`` above that it set to ``pgpassword``). Then, retrieve the IP and the port of the PostgreSQL container, together with the default Orthanc configuration file:: - $ sudo docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres - $ sudo docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres - $ sudo docker run --rm --entrypoint=cat jodogne/orthanc-plugins /etc/orthanc/orthanc.json > /tmp/orthanc.json + $ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres + $ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres + $ docker run --rm --entrypoint=cat jodogne/orthanc-plugins /etc/orthanc/orthanc.json > /tmp/orthanc.json .. highlight:: json @@ -201,7 +201,7 @@ Finally, you can start Orthanc:: - $ sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins + $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins Debugging @@ -212,15 +212,15 @@ For debugging purpose, you can start an interactive bash session as follows:: - $ sudo docker run -i -t --rm --entrypoint=bash jodogne/orthanc - $ sudo docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins + $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc + $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins For developers and power users, the images ``jodogne/orthanc-debug`` contain the Orthanc core compiled in debug mode (i.e. with runtime assertions enabled, and including debugging symbols). A ``gdb`` command-line session can be started as follows:: - $ sudo docker run -i -t --rm --entrypoint=bash --network=host --cap-add=SYS_PTRACE -p 4242:4242 -p 8042:8042 jodogne/orthanc-debug + $ docker run -i -t --rm --entrypoint=bash --network=host --cap-add=SYS_PTRACE -p 4242:4242 -p 8042:8042 jodogne/orthanc-debug # gdb --args Orthanc /etc/orthanc/ --verbose Exceptions can be automatically caught by launching ``gdb`` as follows::